So I just ordered a physical copy of ACNL for cycling, excessive time travel, etc. My current game is a downloaded version, so would anything happen to my town if I put the physical cartridge in and started a new town?
Like everyone else said, be careful! Anytime I've seen posts about people losing their towns or their files being corrupted, it's because of a digital copy. I've seen plenty of people running both a digital copy and a cartridge copy on the same 3ds just fine, but data corruption is a real danger once you start doing this. Just be extra careful, like prostime said.